Widely Targeted Metabolomics Reveals Metabolite Diversity in Jalapeño and Serrano Chile Peppers (Capsicum annuum L.)

Abstract

Chile peppers (Capsicum annuum L.) are good sources of vitamins and minerals that can be included in the diet to mitigate nutritional deficiencies. Metabolomics examines the metabolites involved in biological pathways to understand the genes related to complex phenotypes such as the nutritional quality traits. The current study surveys the different metabolites present in jalapeño ('NuMex Pumpkin Spice') and serrano ('NuMex LotaLutein') type chile peppers grown in New Mexico using a widely targeted metabolomics approach, with the 'NuMex LotaLutein' as control. A total of 1088 different metabolites were detected, where 345 metabolites were differentially expressed; 203 (59%) were downregulated and 142 (41%) were upregulated (i.e., relative metabolite content is higher in 'NuMex Pumpkin Spice'). The upregulated metabolites comprised mostly of phenolic acids (42), flavonoids (22), and organic acids (13). Analyses of principal component (PC) and orthogonal partial least squares demonstrated clustering based on cultivars, where at least 60% of variation was attributed to the first two PCs. Pathway annotation identified 89 metabolites which are involved in metabolic pathways and the biosynthesis of secondary metabolites. Altogether, metabolomics provided insights into the different metabolites present which can be targeted for breeding and selection towards the improvement of nutritional quality traits in Capsicum.

Keywords: flavonoids; human health; nutrition; phenolic acids; ultra-performance liquid chromatography tandem mass spectrometry; ‘NuMex LotaLutein’; ‘NuMex Pumpkin Spice’.

Figure 1

‘Numex Pumpkin Spice’ (a) and ‘NuMex LotaLutein’ (b) fruits showing their characteristic orange and yellow colors, respectively. ‘NuMex Pumpkin Spice’ is a colored jalapeño, whereas ‘NuMex LotaLutein’ is a biofortified serrano type with improved lutein content. Adapted with permission from Refs. [22,23]. ©2015, 2020, American Society for Horticultural Science.

Figure 2

Proportion of different classes of compounds for the metabolites detected from jalapeño and serrano chile peppers using a widely targeted metabolomics approach.

Figure 3

(a) Principal component (PC) biplot for the PC1 and PC2 reveal the overall variation between the cultivars in terms of metabolomic profiles. (b) Orthogonal partial least squares discriminant plot for the chile pepper cultivars. Treatment 1: ‘NuMex LotaLutein’; treatment 2: ‘NuMex Pumpkin Spice’. Numbers 1, 2, and 3 correspond to the first, second, and third biological replications, respectively.

Figure 4

Pearson correlation coefficients among the biological replicates for the cultivars. Numbers 1, 2, and 3 correspond to the first, second, and third biological replications, respectively. Correlation coefficients were significant at p < 0.0001.

Figure 5

Summary of the different functions annotated for the differentially expressed metabolites (DEMs) using the KEGG database. Annotations revealed that the majority of the DEMs are involved in metabolic pathways and in the biosynthesis of secondary metabolites and cofactors. Note: A DEM can have multiple annotated functions.

Figure 6

Rich factor (RF) values for the differentially expressed metabolites with annotated functions on the KEGG database. RF is the ratio of the number of differentially expressed metabolites in a pathway to the total number of metabolites annotated in the same pathway (RF for a pathway = no. of differentially expressed metabolites/total number of metabolites). Terpenoid backbone biosynthesis had significant enrichments, with an RF value of 1.